Satya,
For whatever reason, you are not able to perform complex atom selections
in X-PLOR during patching. [You cannot define BOTH the segid and the
residue number.] I am aware of two options for dealing with this:
1. Renumber each molecule in the asym unit so that each residue has a
unique number. Mol1 might be resid 1-300, mol2 could be 1001-1300, etc.
In this case, use the first syntax that you proposed, just repeat it for
each set of disulfides to form.
2. Run 4 separate topology generation routines, and then read in the
four topology files and four pdb files when you start your refinement.
For this option to work, each molecule will need to have its own segid.
Again, you should use your first example for syntax of the patch
statement. NOTE: correct X-PLOR syntax for segid puts the id in quotes:
(segid "mol1" and resid 2:36)
This will be important for setting up your NCS restraints if you use
them.
Good luck,
Jim
james.r.kiefer at monsanto.com
______________________________ Reply Separator _________________________________
Subject: syntex for 'patch' card
Author: BIOSCI-REQUEST at net.bio.net at INTERNET
Date: 03/24/1999 7:41 PM
Dear Everybody,
I am refining a MR model ( four molecule in the asymmetric
unit e.g. A,B,C and D ) by X-PLOR (Version 3.851). There are two di-sulfide
bridges in each chain.
What is the correct syntex for 'patch' card ?
******************************************************************************
(===>) (*Create S-S bridges.*)
patch disu
reference=1=( resid 23 )
reference=2=( resid 55 )
end
patch disu
reference=1=( resid 125 )
reference=2=( resid 144 )
end
*****************************************************************************
(===>) (*Create S-S bridges.*)
patch disu
reference=1=( segid A and resid 23 )
reference=2=( segid A and resid 55 )
end
patch disu
reference=1=( segid A and resid 125 )
reference=2=( segid A and resid 144 )
end
***************************************************************************
I am just started learning X-plor, please help me.
Thanks in advance.
Satya